In the episode "46 Long" Brendan and Christopher hijacked a Comley Trucking truck and stole a number of DVD players from it. Comley Trucking was under the protection of DiMeo capo Corrado Soprano, who led another crew in the DiMeo crime family. Junior demanded restitution from Christopher and Brendan. At a sit down Junior tells Tony Soprano to keep Brendan and Christopher's "loose cannon" behavior under control, both men answered to Tony as they were in his crew. In a nightclub, Brendan tries his best to convince Christopher to neglect Tony and Uncle Junior since they were both being denied a promotion in the organisation. Early the next morning, Brendan urges Christopher to get ready for the next heist, a truckload of Italian suits. Christopher tells him that he has decided to go along with the rules instead and Brendan goes without him.
High on crystal meth and unable to comply with orders, Brendan, without Christopher, hijacks another Comley truck with two African-American cohorts Special K and Antjuan. In the process, the driver of the second Comley truck is accidentally shot and killed by a ricochet bullet when one of the thugs drops his gun. Once Tony learns about this mishap, Brendan and Christopher receive a lecture about leadership and are ordered to return the truck to Comley. However, Uncle Junior isn't satisfied. DiMeo soldier and Junior's confidant Mikey Palmice gives Junior advice on the matter, telling him he should have dealt with the situation the minute it happened and to send a message not to mess with him. Junior also visits Livia Soprano, Tony's mother, at Green Grove Retirement Home and discusses the Christopher and Brendan situation, complaining that the young associates are causing trouble. Livia points out that both she and Tony love Christopher like a son (her affection was earned one year when Christopher put up her storm windows). She suggests that Junior give Tony's hot-tempered nephew a "talking to" but says that she "doesn't know" about Brendan. Junior compliments Livia on her wise decision-making.
The "talking to" given to Christopher manifests as a mock execution at the hands of Russian goons hired by Junior. Because of Livia's advice, Junior ordered that Christopher receive a mock execution — and a real one for Brendan. Brendan was shot clean through the eye ("Moe Greene special") while in his bathtub by Mikey Palmice, as Junior stood by. Brendan's execution is inter-cut with Meadow's recital, allowing her choir's version of the lullaby "All Through the Night" to decorate the violence.
- In the aftermath, Christopher and his girlfriend Adriana La Cerva find Filone's body in his bathtub and Christopher calls for harsh retaliation against Mikey. Tony tells Christopher not to do anything, because Mickey is a "made man" and Christopher is not. Tony decides to confront his uncle and Mikey for their punishing methods by beating Mikey to the ground and stapling him with some tickets. He then goes to have a sit-down with Uncle Junior for his orders.
- Brendan Filone's last onscreen appearance was in the first season episode "The Legend of Tennessee Moltisanti". He is one of the main concentrations on television when Jeffrey Wernick is interviewed about the murder charges. Wernick reveals that Brendan was a loyal soldier and associate and his murder was as yet unsolved from the eyes of a federal agent. The amount of attention and coverage Filone receives after his demise makes Christopher annoyed and jealous. Even Georgie says that he is amazed to have known Christopher.
- Later when DiMeo capo Jimmy Altieri attends a funeral, he notifies Uncle Junior of how sad Filone's mother was at his funeral. Junior reciprocates by telling Mikey and Chucky Signore about Altieri's remark, noting that this is the kind of things they are talking about behind his back, namely the "Brendan Filone hit."
- Later, in retaliation for the attempted hit on Tony, Mikey Palmice was killed after Christopher and Paulie Gualtieri chased him down while he was jogging. Mikey tried to blame all the recent events on Junior, even Filone's death, but Chris replies, "My friend Brendan, you shot him in his bathtub naked, no chance to run." Paulie and Chris then execute Mikey, leaving him dead in the woods.
- In season two, after Christopher is shot by Sean Gismonte and Matthew Bevilaqua, he has a near-death experience in the hospital where he goes to "purgatory" and explains that he saw Brendan Filone and Mikey Palmice playing cards with a bunch of Roman soldiers and Irish men. Christopher also mentions that Brendan and Palmice are friends in hell although they were enemies when alive.
- Brendan Filone has a collectible trading card (#19) in "The Sopranos: Season One Ultra-Premium Trading Card" series released by Inkworks in July, 2005.
- Brendan's execution scene is a similar montage sequence to the baptism in The Godfather, where a peaceful event unfolds at the same time as mob violence. The method in which Brendan is killed is also a reference to the film, where the character of Moe Greene is shot through the eye.
- Brendan states that he used to be an installer.
- Brendan hits on Meadow and her best friend, Hunter Scangarelo. Hunter herself is attracted to Brendan and responds by nodding at him. She also asks about him, unaware about his execution.